Embedding two plots in manuscripts causes issues

Bug description

I am not sure if this a bug or if manuscripts have been planned to work certain way, but here is report anyway. Hopefully it is helpful!

Steps to reproduce

I have two .qmds, the index and penguins.qmd. The index.qmd is;

---
title: Article
authors:
  - name: Norah Jones
    affiliation: The University
    roles: writing
    corresponding: true
bibliography: references.bib
---

## Section

This is a simple placeholder for the manuscript's main document [@knuth84].

```{r}
#| label: example
1 + 1
```

Embedding single plot cell 

{{< embed notebooks/penguins.qmd#fig-onefig >}}

Some other text here

{{< embed notebooks/penguins.qmd#fig-twofig >}}

and penguins.qmd

---
title: "Subfig"
---

```{r}
#| label: fig-onefig
#| fig-cap: "A plot with a single cap"
# Calculate bill ratio
plot(1)
```
```{r}
#| label: fig-twofig
#| fig-cap: |
#|  First caption
#| fig-subcap: 
#|   - "A"
#|   - "B"
plot(2)
plot(3)
```

_quarto.yml is

project:
  type: manuscript

execute:
  freeze: false

format:
  html:
    toc: true
    comments:
      hypothesis: true

Trying to embed the cell labeled fig-charts with two ggplots causes issue.

Expected behavior

The two plots are embedded into the index.qmd and rendered.

Actual behavior

Rendering qmd embeds [notebooks\penguins.qmd]
Error running filter C:/PROGRA~1/Quarto/share/filters/main.lua:
Block, list of Blocks, or compatible element expected, got Blocks
	while retrieving function argument content
	while retrieving arguments for function Div
stack traceback:
	C:/PROGRA~1/Quarto/share/filters/main.lua:23206: in field 'render'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1233: in local 'filter_fn'
	C:/PROGRA~1/Quarto/share/filters/main.lua:635: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:625>
	(...tail calls...)
	[C]: in ?
	[C]: in method 'walk'
	C:/PROGRA~1/Quarto/share/filters/main.lua:557: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:546>
	(...tail calls...)
	C:/PROGRA~1/Quarto/share/filters/main.lua:1334: in local 'callback'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1388: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:1385>
stack traceback:
	C:/PROGRA~1/Quarto/share/filters/main.lua:557: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:546>
	(...tail calls...)
	C:/PROGRA~1/Quarto/share/filters/main.lua:1334: in local 'callback'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1388: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:1385>
	
removing the layout-ncol: 2 sometimes gives

Block, list of Blocks, or compatible element expected, got table
	while retrieving function argument content
	while retrieving arguments for function Div
stack traceback:
	C:/PROGRA~1/Quarto/share/filters/main.lua:22445: in field 'render'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1233: in local 'filter_fn'
	C:/PROGRA~1/Quarto/share/filters/main.lua:635: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:625>
	(...tail calls...)
	[C]: in ?
	[C]: in method 'walk'
	C:/PROGRA~1/Quarto/share/filters/main.lua:557: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:546>
	(...tail calls...)
	C:/PROGRA~1/Quarto/share/filters/main.lua:1334: in local 'callback'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1388: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:1385>
stack traceback:
	C:/PROGRA~1/Quarto/share/filters/main.lua:557: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:546>
	(...tail calls...)
	C:/PROGRA~1/Quarto/share/filters/main.lua:1334: in local 'callback'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	C:/PROGRA~1/Quarto/share/filters/main.lua:1388: in function <C:/PROGRA~1/Quarto/share/filters/main.lua:1385>

Your environment

RStudio "Chocolate Cosmos" Release (e4392fc9, 2024-06-05) for windows
Quarto Quarto 1.6.3, also tested with 1.5 and could repo the issue

Quarto check output

Quarto 1.6.3
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.6.3
      Path: C:\Program Files\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: v2024.07.03
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\X\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2024

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
      Version: 3.11.2
      Path: C:/Users/X/AppData/Local/Programs/Python/Python311/python.exe
      Jupyter: 5.7.2
      Kernels: python3

[>] Checking Jupyter engine render....OK

[>] Checking R installation...........OK
      Version: 4.4.1
      Path: C:/PROGRA~1/R/R-44~1.1
      LibPaths:
        - C:/Users/X/AppData/Local/R/win-library/4.4
        - C:/Program Files/R/R-4.4.1/library
      knitr: 1.48
      rmarkdown: 2.27

[>] Checking Knitr engine render......OK

```
also gives the warning WARN: Error removing file and more spefically (os error 32) about removing a file because it used by another process, the message is in system language so didnt include it here